Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011807.1 Corchorus olitorius cultivar O-4 contig11840, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 815
Length: 1359
ACGTcount: A:0.24, C:0.28, G:0.28, T:0.20
Found at i:973 original size:33 final size:33
Alignment explanation
Indices: 936--1275 Score: 197
Period size: 33 Copynumber: 9.6 Consensus size: 33
926 GTTGCCAAGC
936 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
**
969 GCCATCGGCAAGTCCCGAGTGCCATCGGCAACTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTG---T---CAA-GGCCGAGT
* * * *
1009 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGT
1 GCCATCGG-CAAGTCCCGAGT-GTCAAG-GCCGAGT
* * * *
1042 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGT
1 GCCATCGG-CAAGTCCCGAGT-GTCAAG-GCCGAGT
** *
1075 GCCATCGGCAAGTGTCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTG---T---CAAG-GCCGAGT
*
1115 GCCGATCGGCAAGTCCCGAGTGCCAAGGCCGAGT
1 GCC-ATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
* *
1149 GCCATCAGCAAGTCCCGAGTGCCAAGGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
** *
1182 GCCATCGGCAAGTGTCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTG---T---CAAG-GCCGAGT
*
1222 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
*
1255 GCCATCGGCAAGTCTCGAGTG
1 GCCATCGGCAAGTCCCGAGTG
1276 CCATCGGCAA
Statistics
Matches: 252, Mismatches: 28, Indels: 54
0.75 0.08 0.16
Matches are distributed among these distances:
33 146 0.58
34 17 0.07
35 5 0.02
36 1 0.00
38 1 0.00
39 11 0.04
40 55 0.22
41 16 0.06
ACGTcount: A:0.21, C:0.32, G:0.32, T:0.15
Consensus pattern (33 bp):
GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGT
Found at i:1005 original size:53 final size:53
Alignment explanation
Indices: 936--1359 Score: 404
Period size: 53 Copynumber: 8.0 Consensus size: 53
926 GTTGCCAAGC
* *
936 GCCATCGGCAAGTCCCGAGTGTCAAGGCCGAGTGCCATCGGCAAGTCCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
* *
989 GCCATCGGCAACTCCCGAGTGCCAAGGCCTAGTGCCATCGGCAAGTGCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
* * * * *
1042 GCCA-AGGCCTAGTGCC-A-TCGGCAAGTGCCGAGTGCCATCGGCAAGTGTCGAGT
1 GCCATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGTGCCATCGGCAAGTGCCGAGT
* * * *
1095 GCCATCGGCAAGTCCCGAGTGCCGATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCC-A-AGGCCGAGTGCC-A-TCGGCAAGTGCCGAGT
* *
1149 GCCATCAGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGTCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
* * * *
1202 GCCATCGGCAAGTCCCGAGTGCCATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCA-AGGCCGAGTGCC-A-TCGGCAAGTGCCGAGT
* * * * *
1255 GCCATCGGCAAGTCTCGAGTGCCATCGG-CAAGTCCCGAGT-GCCAAG-GCCGAGT
1 GCCATCGGCAAGTCCCGAGTGCCA-AGGCCGAGTGCC-A-TCGGCAAGTGCCGAGT
* **
1308 GCCATCGGCATGTCCCGAGTGCTTAGGCCGAGTGCCATCGGCAAGTGCCGAG
1 GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAG
Statistics
Matches: 311, Mismatches: 41, Indels: 38
0.80 0.11 0.10
Matches are distributed among these distances:
51 3 0.01
52 24 0.08
53 225 0.72
54 47 0.15
55 10 0.03
56 2 0.01
ACGTcount: A:0.21, C:0.32, G:0.33, T:0.15
Consensus pattern (53 bp):
GCCATCGGCAAGTCCCGAGTGCCAAGGCCGAGTGCCATCGGCAAGTGCCGAGT
Found at i:1307 original size:33 final size:33
Alignment explanation
Indices: 1270--1359 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
1260 CGGCAAGTCT
1270 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGC
* **
1303 CGAGTGCCATCGGCATGTCCCGAGTGCTTAGGC
1 CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGC
*
1336 CGAGTGCCATCGGCAAGTGCCGAG
1 CGAGTGCCATCGGCAAGTCCCGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.19, C:0.31, G:0.34, T:0.16
Consensus pattern (33 bp):
CGAGTGCCATCGGCAAGTCCCGAGTGCCAAGGC
Found at i:1359 original size:20 final size:20
Alignment explanation
Indices: 958--1298 Score: 279
Period size: 20 Copynumber: 18.8 Consensus size: 20
948 TCCCGAGTGT
958 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
977 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
* *
997 CAACTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1011 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1030 CAAGTGCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1044 CAAG-GCCTAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1063 CAAGTGCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1083 CAAGTGTCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1103 CAAGTCCCGAGTGCCGATCGG
1 CAAGTGCCGAGTGCC-ATCGG
*
1124 CAAGTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
*
1138 CAAG-GCCGAGTGCCATCAG
1 CAAGTGCCGAGTGCCATCGG
*
1157 CAAGTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
1171 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1190 CAAGTGTCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1210 CAAGTCCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
*
1230 CAAGTCCCGAGTG----C--
1 CAAGTGCCGAGTGCCATCGG
1244 CAAG-GCCGAGTGCCATCGG
1 CAAGTGCCGAGTGCCATCGG
1263 CAAGT-CTCGAGTGCCATCGG
1 CAAGTGC-CGAGTGCCATCGG
*
1283 CAAGTCCCGAGTGCCA
1 CAAGTGCCGAGTGCCA
1299 AGGCCGAGTG
Statistics
Matches: 265, Mismatches: 18, Indels: 77
0.74 0.05 0.21
Matches are distributed among these distances:
13 34 0.13
14 19 0.07
16 5 0.02
17 5 0.02
19 25 0.09
20 158 0.60
21 19 0.07
ACGTcount: A:0.21, C:0.32, G:0.32, T:0.15
Consensus pattern (20 bp):
CAAGTGCCGAGTGCCATCGG
Done.